I think you need to apply the negative to the word it is affecting in the sentence.
These are closer in meaning but each relates to either side of neutrality.
It's nice not to be rude
Is a bit more positive/complimentary - you are saying that by simply not being rude you are being nice.
It isn't nice to be rude
In this case you're not making any comment about not being rude (e.g. - you might have to do a bit more work than just not be rude if you want to be nice). But certainly if you are rude, you are not being nice.
It's a bit more clear with your second group.
I decided not to come.
Here you made a decision - that you were not going to come.
I didn't decide to come.
Whereas here you did not necessarily make a decision.